123 lines
4.3 KiB
Groff
123 lines
4.3 KiB
Groff
LAMMPS (15 Sep 2022)
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using 1 OpenMP thread(s) per MPI task
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# Vesicle demo
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variable T equal 0.2
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variable LD equal 1.0
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units lj
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atom_style ellipsoid
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boundary p p p
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read_data read_data.vesicle1026
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Reading data file ...
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orthogonal box = (-35 -35 -35) to (35 35 35)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2938 atoms
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2938 ellipsoids
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read_data CPU = 0.137 seconds
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compute ali all temp/com
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compute rott all temp/asphere bias ali
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velocity all create ${T} 87287 loop geom
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velocity all create 0.2 87287 loop geom
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pair_style ylz 2.6
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pair_coeff * * 1.0 1.0 4 3 0.0 2.6
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neighbor 1.0 bin
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thermo_style custom step temp press pxx pyy
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thermo 200
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timestep 0.001
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#dump 1 all atom 10 onlymembrane2.lammpstrj
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 1 all langevin 0.2 ${T} ${LD} 48279
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fix 1 all langevin 0.2 0.2 ${LD} 48279
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fix 1 all langevin 0.2 0.2 1 48279
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fix 2 all nve/asphere
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run 3000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- pair ylz command:
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@Article{Yuan10,
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author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
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title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
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journal = {Phys. Rev. E},
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year = 2010,
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volume = 82,
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pages = {011905}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 10 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.6
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ghost atom cutoff = 3.6
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binsize = 1.8, bins = 39 39 39
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair ylz, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.899 | 4.9 | 4.902 Mbytes
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Step Temp Press Pxx Pyy
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0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
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200 0.12893798 -0.0051492794 -0.0048734875 -0.0049624005
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400 0.13798694 -0.004875313 -0.0047071897 -0.0049305051
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600 0.14725193 -0.0046349542 -0.004719983 -0.0045791451
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800 0.16146954 -0.0042232199 -0.0040789193 -0.0043672895
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1000 0.17268468 -0.0037146703 -0.0036270393 -0.0039169034
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1200 0.18266242 -0.0032749755 -0.0032971704 -0.0033323855
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1400 0.18500165 -0.0028179031 -0.0030659821 -0.0027519633
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1600 0.19513132 -0.0023407512 -0.0025109801 -0.0023416835
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1800 0.19645259 -0.0019995412 -0.0019064341 -0.0021757747
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2000 0.19658104 -0.0015897919 -0.0015850523 -0.0016828478
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2200 0.1989936 -0.0011794062 -0.0011779716 -0.0012070706
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2400 0.20011525 -0.0009147432 -0.00094040885 -0.001073922
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2600 0.2013975 -0.00059253676 -0.00051920304 -0.00075138934
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2800 0.19715513 -0.00020995605 -0.00024386426 -0.0005475745
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3000 0.1976782 -0.0001308553 5.693004e-05 -0.00034478469
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Loop time of 8.46954 on 4 procs for 3000 steps with 2938 atoms
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Performance: 30603.800 tau/day, 354.211 timesteps/s
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77.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.1751 | 2.4162 | 2.6707 | 13.2 | 28.53
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Neigh | 0.0090503 | 0.0098389 | 0.010503 | 0.6 | 0.12
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Comm | 3.5807 | 4.1526 | 4.9283 | 24.3 | 49.03
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Output | 0.00032165 | 0.0029648 | 0.010842 | 8.4 | 0.04
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Modify | 0.34554 | 0.37442 | 0.39198 | 2.8 | 4.42
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Other | | 1.514 | | | 17.87
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Nlocal: 734.5 ave 739 max 730 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Nghost: 420.25 ave 424 max 415 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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Neighs: 18304.5 ave 19839 max 16636 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Total # of neighbors = 73218
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Ave neighs/atom = 24.921035
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Neighbor list builds = 25
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Dangerous builds = 0
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Total wall time: 0:00:08
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